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991.
Karsten Schnatbaum Victor Solis‐Mezarino Daniil Pokrovsky Frederike Schfer Dennis Nagl Lars Hornberger Johannes Zerweck Tobias Knaute Julia Avramova‐Nehmer Mike Schutkowski Veit Hornung Holger Wenschuh Moritz Carl Vlker‐Albert Axel Imhof Ulf Reimer 《Proteomics》2020,20(10)
Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re‐quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2. 相似文献
992.
Liya Ming Yang Zou Yiming Zhao Luna Zhang Ningning He Zhen Chen Shawn S.‐C. Li Lei Li 《Proteomics》2020,20(15-16)
A large number of post‐translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot‐gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non‐modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide‐spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large‐scale proteomics datasets generated by liquid chromatography‐MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL‐3 license. 相似文献
993.
Ten‐Yang Yen Richard Wong Donald Pizzo Moe Thein Bruce A. Macher Leslie C. Timpe 《Proteomics》2020,20(15-16)
This study identifies the main changes in protein expression in human breast tumors compared to normal breast tissue. Malignant tumors (32) and normal breast tissue samples (23), from formaldehyde‐fixed, paraffin‐embedded specimens are subjected to discovery proteomics using liquid chromatography/tandem mass spectrometry, with spectral counts for quantitation. The dataset contains 1406 proteins. Differential expression is measured using a method that takes advantage of estimates of the percentage of tumor on a slide. This analysis shows that the major classes of proteins over‐expressed by tumors are RNA‐binding, heat shock and DNA repair proteins. RNA‐binding proteins, including heterogeneous nuclear ribonucleoproteins (HNRNPs), SR splice factors (SRSF) and elongation factors form the largest group. Comparison with results from another study demonstrates that the RNA‐binding proteins are associated specifically with malignant transformation, rather than with cell proliferation. HNRNP and SRSF proteins help define splice sites in normal cells. Their over‐expression may dysregulate splicing, which in turn has the potential to promote malignant transformation. 相似文献
994.
Alfredo Floristn Leah Morales Douglas Hanniford Carlos Martinez Elena Castellano‐Sanz Igor Dolgalev Alejandro Ulloa‐Morales Eleazar Vega‐Saenz de Miera Una Moran Farbod Darvishian Iman Osman Tomas Kirchhoff Eva Hernando 《Pigment cell & melanoma research》2020,33(3):466-479
Next‐generation sequencing has enabled genetic and genomic characterization of melanoma to an unprecedent depth. However, the high mutational background plus the limited depth of coverage of whole‐genome sequencing performed on cutaneous melanoma samples make the identification of novel driver mutations difficult. We sought to explore the somatic mutation portfolio in exonic and gene regulatory regions in human melanoma samples, for which we performed targeted sequencing of tumors and matched germline DNA samples from 89 melanoma patients, identifying known and novel recurrent mutations. Two recurrent mutations found in the RPS27 promoter associated with decreased RPS27 mRNA levels in vitro. Data mining and IHC analyses revealed a bimodal pattern of RPS27 expression in melanoma, with RPS27‐low patients displaying worse prognosis. In vitro characterization of RPS27‐high and RPS27‐low melanoma cell lines, as well as loss‐of‐function experiments, demonstrated that high RPS27 status provides increased proliferative and invasive capacities, while low RPS27 confers survival advantage in low attachment and resistance to therapy. Additionally, we demonstrate that 10 other cancer types harbor bimodal RPS27 expression, and in those, similarly to melanoma, RPS27‐low expression associates with worse clinical outcomes. RPS27 promoter mutation could thus represent a mechanism of gene expression modulation in melanoma patients, which may have prognostic and predictive implications. 相似文献
995.
Muriel Cario Catherine Pain Priscilla Kaulanjan‐Checkmodine Daniela Masia Gabriele Delia Vincent Casoli Pierre Costet Jean‐Franois Goussot Vronique Guyonnet‐Duperat Alice Bibeyran Khaled Ezzedine Corinne Reymermier Valrie Andre‐Frei Alain Taieb 《Pigment cell & melanoma research》2020,33(3):435-445
Human skin melanin pigmentation is regulated by systemic and local factors. According to the type of melanin produced by melanocytes, the transfer and degradation of melanosomes differ, thus accounting for most variations between ethnicities. We made the surprising observation that in a drastically changed environment, white and black phenotypes are reversible since Caucasian skin grafted onto nude mice can become black with all black phenotypic characteristics. Black xenografts differed essentially from other grafts by the levels of epidermal FGF‐2 and keratin 5. In vitro analysis confirmed that FGF‐2 directly regulates keratin 5. Interestingly, this phenomenon may be involved in human pathology. Keratin 5 mutations in Dowling–Degos Disease (DDD) have already been associated with the pheomelanosome–eumelanosome transition. In a DDD patient, keratin 5 was expressed in the basal and spinous layers, as observed in black xenografts. Furthermore, in a common age‐related hyperpigmentation disorder like senile lentigo (SL), keratin 5 distribution is also altered. In conclusion, modulation of keratin 5 expression and distribution either due to mutations or factors may account for the development of pigmentary disorders. 相似文献
996.
Weihua Ma Xianxin Zhao Chuanlin Yin Fan Jiang Xiaoyong Du Taiyu Chen Qinghua Zhang Lin Qiu Hongxing Xu J. Joe Hull Guoliang Li Wing‐Kin Sung Fei Li Yongjun Lin 《Molecular ecology resources》2020,20(1):268-282
The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant–insect interactions, pesticide targets and resistance, and the development of RNAi‐mediated pest management, the absence of a high‐quality genome has limited deeper insights. To address this limitation, we generated a draft C. suppressalis genome constructed from both Illumina and PacBio sequences. The assembled genome size was 824.35 Mb with a contig N50 of 307 kb and a scaffold N50 of 1.75 Mb. Hi‐C scaffolding assigned 99.2% of the bases to one of 29 chromosomes. Based on universal single‐copy orthologues (BUSCO), the draft genome assembly was estimated to be 97% complete and is predicted to encompass 15,653 protein‐coding genes. Cold tolerance is an extreme survival strategy found in animals. However, little is known regarding the genetic basis of the winter ecology of C. suppressalis. Here, we focused our orthologous analysis on those gene families associated with animal cold tolerance. Our finding provided the first genomic evidence revealing specific cold‐tolerant strategies in C. suppressalis, including those involved in glucose‐originated glycerol biosynthesis, triacylglycerol‐originated glycerol biosynthesis, fatty acid synthesis and trehalose transport‐intermediate cold tolerance. The high‐quality C. suppressalis genome provides a valuable resource for research into a broad range of areas in molecular ecology, and subsequently benefits developing modern pest control strategies. 相似文献
997.
Dave Lutgen Raphael Ritter Remi‐Andr Olsen Holger Schielzeth Joel Gruselius Philip Ewels Jesús T. García Hadoram Shirihai Manuel Schweizer Alexander Suh Reto Burri 《Molecular ecology resources》2020,20(5):1311-1322
The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps – are still limited by the lack of high‐quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype‐resolved genome resequencing at population scale, we investigated properties of linked‐read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25×, 20×, 15×, 10×, 7×, and 5×) with high‐coverage data (46–68×) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15× coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25–4.6 Mb (N50) and 0.27–0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15× coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25× coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher‐quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase‐sized genomes like birds, linked‐read sequencing at moderate depth opens an affordable avenue towards haplotype‐resolved genome resequencing at population scale. 相似文献
998.
Youngkyoung Lim Hyun‐Tae Shin YoungHwan Choi Dong‐Youn Lee 《Pigment cell & melanoma research》2020,33(2):318-325
Melanoma can develop in a congenital melanocytic nevus (CMN). In fact, a large CMN is associated with a high risk of developing melanoma. Although melanomas arising from CMNs are thought to have a pathogenesis distinct from conventional melanomas, no studies have been conducted on the evolution or tumor heterogeneity of CMN melanomas. We applied multi‐region whole‐exome sequencing to investigate the clonal nature of driver events and evolutionary processes in CMNs and melanomas arising from CMNs. In two patients, we observed an independent subclonal evolution in cancerized fields of CMNs and chromosome 8q amplification in both melanomas arising from CMNs. The amplification of MYC, located in chromosome 8q, was correlated with the percentage of tumor cells expressing high levels of MYC protein detected in melanoma cells by immunohistochemistry. Our analysis suggests that each CMN cell may evolve sporadically and that amplification of MYC might be a key event for melanoma development in CMNs. 相似文献
999.
Ryan J. Quinn HakSoo Ha Timothy A. Volk Tristan R. Brown Steven Bick Robert W. Malmsheimer Marie‐Odile P. Fortier 《Global Change Biology Bioenergy》2020,12(9):728-741
Life cycle assessment (LCA) was combined with primary data from nine forest harvesting operations in New York, Maine, Massachusetts, and Vermont, from 2013 to 2019 where forest biomass (FB) for bioenergy was one of several products. The objective was to conduct a data‐driven study of greenhouse gas emissions associated with FB feedstock harvesting operations in the Northeast United States. Deterministic and stochastic LCA models were built to simulate the current FB bioenergy feedstock supply chain in the Northeast US with a cradle‐to‐gate scope (forest harvest through roadside loading) and a functional unit of 1.0 Mg of green FB feedstock at a 50% moisture content. Baseline LCA, sensitivity analysis, and uncertainty analyses were conducted for three different FB feedstock types—dirty chips, clean chips, and grindings—enabling an empirically driven investigation of differences between feedstock types, individual harvesting process contributions, and literature comparisons. The baseline LCA average impacts were lower for grindings (4.57 kg CO2eq/Mg) and dirty chips (7.16 kg CO2eq/Mg) than for clean chips (23.99 kg CO2eq/Mg) under economic allocation, but impacts were of similar magnitude under mass allocation, ranging from 24.42 to 27.89 kg CO2eq/Mg. Uncertainty analysis showed a wider range of probable results under mass allocation compared to economic allocation. Sensitivity analysis revealed the impact of variations in the production masses and total economic values of primary products of forest harvests on the LCA results due to allocation of supply chain emissions. The high variability in fuel use between logging contractors also had a distinct influence on LCA results. The results of this study can aid decision‐makers in energy policy and guide emissions reductions efforts while informing future LCAs that expand the system boundary to regional FB energy pathways, including electricity generation, transportation fuels, pellets for heat, and combined heat and power. 相似文献
1000.
The United States Great Lakes Region (USGLR) is a critical geographic area for future bioenergy production. Switchgrass (Panicum virgatum) is widely considered a carbon (C)‐neutral or C‐negative bioenergy production system, but projected increases in air temperature and precipitation due to climate change might substantially alter soil organic C (SOC) dynamics and storage in soils. This study examined long‐term SOC changes in switchgrass grown on marginal land in the USGLR under current and projected climate, predicted using a process‐based model (Systems Approach to Land‐Use Sustainability) extensively calibrated with a wealth of plant and soil measurements at nine experimental sites. Simulations indicate that these soils are likely a net C sink under switchgrass (average gain 0.87 Mg C ha?1 year?1), although substantial variation in the rate of SOC accumulation was predicted (range: 0.2–1.3 Mg C ha?1 year?1). Principal component analysis revealed that the predicted intersite variability in SOC sequestration was related in part to differences in climatic characteristics, and to a lesser extent, to heterogeneous soils. Although climate change impacts on switchgrass plant growth were predicted to be small (4%–6% decrease on average), the increased soil respiration was predicted to partially negate SOC accumulations down to 70% below historical rates in the most extreme scenarios. Increasing N fertilizer rate and decreasing harvest intensity both had modest SOC sequestration benefits under projected climate, whereas introducing genotypes better adapted to the longer growing seasons was a much more effective strategy. Best‐performing adaptation scenarios were able to offset >60% of the climate change impacts, leading to SOC sequestration 0.7 Mg C ha?1 year?1 under projected climate. On average, this was 0.3 Mg C ha?1 year?1 more C sequestered than the no adaptation baseline. These findings provide crucial knowledge needed to guide policy and operational management for maximizing SOC sequestration of future bioenergy production on marginal lands in the USGLR. 相似文献